<br> I did try changing the bond length but it wouldn't catch all the disulfides. I do have multiple chains but I don't believe they should be merged. My current work around is to just leave the disulfide residues named CYX according to the amber format and then change them to CYS2 in the .itp files for the corresponding .top file. This way pdb2gmx doesn't protonate the disulfide residues and the charges for CYS2 are maintained. If anyone thinks this is not a good idea, please tell me.
<br><br>Thanks,<br>Russell<br><br><div><span class="gmail_quote">On 7/2/07, <b class="gmail_sendername">Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi Russel,<br><br>You never mentioned the distance between the<br>'sulphurs-that-wouldn't-connect'. Are they beyond the range normal for<br>disulphide bonds? If so, you could try to add an additional entry in<br>
the specbond.dat file with a different bond length. Maybe you'll have<br>to change the residue name first, although it could work without (I<br>don't know whether pdb2gmx properly handles multiple multiple<br>distances for the same atom pair, but it's easy to find out).
<br>Another thing you never mentioned is whether the cysteines are from<br>one chain or from different chains. In the latter case, you have to<br>use the option -merge with pdb2gmx. pdb2gmx will not usually make<br>bonds between different chains.
<br><br>Hope this helps,<br><br>Tsjerk<br><br>On 7/1/07, David van der Spoel <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:<br>> Russell Green wrote:<br>> > Hello,<br>> ><br>> > I just changed the disulfide max bond length in the
specbond.dat file to<br>> > various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some<br>> > of the disulfides in my protein but not all. If I use 0.4, it finds 22<br>> > of the 52 CYS residues to be in disulfide bonds when all 52 should be in
<br>> > disulfide bonds. And, if I use higher bond lengths the number of<br>> > disulfide CYS found decreases. Where should I look next to sort out this<br>> > problem?<br>><br>> pdb2gmx will only make the bonds if they are within 10% of the
<br>> equilibrium length (0.2 nm).<br>> ><br>> > Thanks,<br>> > Russell Green<br>> ><br>> > On 7/1/07, *Mark Abraham* <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>
<br>> > <mailto:<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>>> wrote:<br>> ><br>> ><br>> > Did you use specbond.dat correctly?<br>> > <a href="http://wiki.gromacs.org/index.php/specbond.dat">
http://wiki.gromacs.org/index.php/specbond.dat</a><br>> ><br>> > Mark<br>> ><br>> > _______________________________________________<br>> > gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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<br>><br>><br>> --<br>> David van der Spoel, Ph.D.<br>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
<br>> <a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a> <a href="mailto:spoel@gromacs.org">spoel@gromacs.org</a> <a href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a><br>> _______________________________________________
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><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623
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